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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Mar 12, 2016 |
| Title |
46c_H3K122ac_rep2 |
| Sample type |
SRA |
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| Source name |
46c_H3K122ac
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| Organism |
Mus musculus |
| Characteristics |
cell line: 46c (sox1-GFP)
cell type: mouse embryonic stem cells
passages: 25-28
chip antibody: anti-H3K122ac (Tropberger et al 2013, PMID: 23415232)
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| Treatment protocol |
Undifferentiated ESCs and K562 cells
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| Growth protocol |
46c (Sox1-GFP) ESCs (Ying et al. Nature biotechnology 2003) were cultivated without feeders in GMEM media containing With L-Glutamine media containing 10% fetal bovine serum (FBS), L-glutamine, Sodium Pyruvate, Lif, beta-Mercaptoethanol, Nonessential aminoacids, penicillin and streptomycin. Human erythro-myeloblastoid leukemia cells (K562) were cultured in RPMI 1640 With L-Glutamine media containing 10% fetal bovine serum (FBS), L-glutamine, penicillin and streptomycin.
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
Chromatin was digested with MNase and released at 4C overnight, then histone-DNA complexes were isolated with antibody
DNA libraries were prepared for sequencing using standard Illumina protocols
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| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2500 |
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| Description |
processed data file:
46C_H3K122acmerged.10bpres.bed, 46C_H3K122acmerged.10bpres.bedGraph.gz
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| Data processing |
ChIP-seq reads were aligned to the mm9 genome assembly using bowtie-0.12.8 (options bowtie -e 40 -m 1 -v 2)
Bedgraph tracks were generated from the aligned reads by the program makeUCSC file from HOMER software suite (version 4.3) at a resolution of 10bp and the total number of tags is normalized to 10 million.
bed peak files were generated using SICER (v1.1) (Zang et al, 2009), using GSM1156619 UD46c input as control library, a window size of 200bp, gap size of 600bp and and FDR of 0.01
column headers for islands-summary-FDR0.01.bed files;
chrom,start,end,ChIP_island_read_count,CONTROL_island_read_count,p_value,fold_change,FDR_threshold
Genome_build: 46c data: NCBI37/mm9; K562 data: GRCh37/hg19
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| Submission date |
Feb 04, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Pradeepa M Madapura |
| E-mail(s) |
p.m.madapura@qmul.ac.uk, manthankumar.patel@qmul.ac.uk
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| Organization name |
Queen Mary University of London
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| Lab |
Pradeepa Madapura
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| Street address |
4 Newark Street, Whitechapel
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| City |
London |
| State/province |
UK |
| ZIP/Postal code |
E1 2AT |
| Country |
United Kingdom |
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| Platform ID |
GPL17021 |
| Series (1) |
| GSE66023 |
Histone H3 globular domain acetylation identifies new class of enhancers |
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| Relations |
| BioSample |
SAMN04456551 |
| SRA |
SRX1560888 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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